--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/12 20:54:10	1174
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/27 00:48:12	1198
@@ -948,7 +948,37 @@ void SimSetup::gatherInfo(void){
 
     info[i].useInitXSstate = globals->getUseInitXSstate();
     info[i].orthoTolerance = globals->getOrthoBoxTolerance();
-    
+
+    // check for thermodynamic integration
+    if (globals->getUseThermInt()) {
+      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
+	info[i].useThermInt = globals->getUseThermInt();
+	info[i].thermIntLambda = globals->getThermIntLambda();
+	info[i].thermIntK = globals->getThermIntK();
+	
+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
+	info[i].restraint = myRestraint;
+      }
+      else {
+	sprintf(painCave.errMsg,
+		"SimSetup Error:\n"
+		"\tKeyword useThermInt was set to 'true' but\n"
+		"\tthermodynamicIntegrationLambda (and/or\n"
+		"\tthermodynamicIntegrationK) was not specified.\n"
+		"\tPlease provide a lambda value and k value in your .bass file.\n");
+	painCave.isFatal = 1;
+	simError();    
+      }
+    }
+    else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
+	sprintf(painCave.errMsg,
+		"SimSetup Warning: If you want to use Thermodynamic\n"
+		"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
+		"\tThe useThermInt keyword is 'false' by default, so your\n"
+		"\tlambda and/or k values are being ignored.\n");
+	painCave.isFatal = 0;
+	simError();   
+    }
   }
   
   //setup seed for random number generator
@@ -1261,6 +1291,28 @@ void SimSetup::makeOutNames(void){
         }
       }
 
+      strcpy(info[k].rawPotName, inFileName);
+      nameLength = strlen(info[k].rawPotName);
+      endTest = &(info[k].rawPotName[nameLength - 5]);
+      if (!strcmp(endTest, ".bass")){
+        strcpy(endTest, ".raw");
+      }
+      else if (!strcmp(endTest, ".BASS")){
+        strcpy(endTest, ".raw");
+      }
+      else{
+        endTest = &(info[k].rawPotName[nameLength - 4]);
+        if (!strcmp(endTest, ".bss")){
+          strcpy(endTest, ".raw");
+        }
+        else if (!strcmp(endTest, ".mdl")){
+          strcpy(endTest, ".raw");
+        }
+        else{
+          strcat(info[k].rawPotName, ".raw");
+        }
+      }
+
 #ifdef IS_MPI
 
     }
@@ -1479,7 +1531,7 @@ void SimSetup::mpiMolDivide(void){
   }
   local_SRI = local_bonds + local_bends + local_torsions;
 
-  info[0].n_atoms = mpiSim->getMyNlocal();  
+  info[0].n_atoms = mpiSim->getLocalNatoms();  
   
 
   if (local_atoms != info[0].n_atoms){